Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A26 F60 I1 R1 14 64.5 2212006 99.2% 2194309 139.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,815,883 +C coding (667/687 nt) rph ← truncated RNase PH

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,815,8791.C95.9% 168.4 / ‑0.3 49coding (671/687 nt)rphtruncated RNase PH
Reads supporting (aligned to +/- strand):  ref base . (2/0);  new base C (20/27);  total (22/27)
Fisher's exact test for biased strand distribution p-value = 1.96e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATT‑C‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCT  >  NC_000913/3815741‑3816013
                                                                                                                                           |                                                                                                                                        
cAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGgattcgatt‑c                                                                                                                                         <  1:126042/140‑1 (MQ=255)
     aaCTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATT‑c‑c‑ccct                                                                                                                                  <  1:1021804/140‑3 (MQ=255)
           cgcTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTAAAAGGGATTCGATTCC‑C‑CCTCGGGcc                                                                                                                             >  1:342490/1‑140 (MQ=255)
                  atGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCca                                                                                                                      >  2:927406/1‑140 (MQ=255)
                    ggTTTCATGCCTTCGCTTCTCATCTTACTTTTCTATAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCcaac                                                                                                                    <  2:425119/140‑1 (MQ=255)
                     gTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCcaaca                                                                                                                   >  1:571333/1‑140 (MQ=255)
                          aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATg                                                                                                              >  2:760156/1‑140 (MQ=255)
                          aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATg                                                                                                              >  1:101453/1‑140 (MQ=255)
                          aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATg                                                                                                              >  2:873889/1‑140 (MQ=255)
                          aTGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATg                                                                                                              >  1:1095037/1‑140 (MQ=255)
                          aTGCCTTCGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGa                                                                                                             >  1:19949/1‑140 (MQ=255)
                           tGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGcc                                                                                                                             <  2:705301/124‑1 (MQ=255)
                           tGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGcc                                                                                                                             >  1:705301/1‑124 (MQ=255)
                           tGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAg                                                                                                                 >  2:120024/1‑136 (MQ=255)
                           tGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAg                                                                                                                 <  1:120024/136‑1 (MQ=255)
                           tGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGa                                                                                                             <  2:1095037/140‑1 (MQ=255)
                               ttCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACATTGGATTCGATT‑C‑CGCCTAGGACCAGAGTCAACAAGATGAGTAg                                                                                                         >  1:325831/1‑140 (MQ=255)
                               ttCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                         <  1:927406/140‑1 (MQ=255)
                               ttCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                         <  2:101453/140‑1 (MQ=255)
                               ttCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                         <  1:795350/140‑1 (MQ=255)
                               ttCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAg                                                                                                         <  1:579799/140‑1 (MQ=255)
                                tCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGc                                                                                                        >  1:242165/1‑140 (MQ=255)
                                tCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCGACAATGGAGTCGATA‑CGC‑CCTCGGGGCAGAACCAACAAGTTGAGTAGc                                                                                                        >  2:534267/1‑140 (MQ=255)
                                tCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCAACAATGGAATCGTTTCC‑C‑CCTCGGGCCAGACCCAACAAGATGAGTAGc                                                                                                        >  2:358832/1‑140 (MQ=255)
                                 cGCTCCTCATCTTACTTTTCTACAGAC‑AAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAGGATGAGTAGctc                                                                                                      <  2:1021443/140‑1 (MQ=255)
                                    tcctcATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCtt                                                                                                    <  1:873889/140‑1 (MQ=255)
                                      ctcATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCa                                                                                                  <  2:948959/140‑1 (MQ=255)
                                        cATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATg                                                                                                >  2:552429/1‑140 (MQ=255)
                                                   tCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCACCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCTGAGACAACAAGATGAGTAGCTTTTCATGGGTGAACGGcc                                                                                     >  2:391635/1‑139 (MQ=255)
                                                     tACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCg                                                                                   >  1:43483/1‑140 (MQ=255)
                                                         gACAAAAAAAAGGCGTCTCATCTGTTGCCCTAAAAATGAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCtt                                                                               <  1:534267/140‑1 (MQ=255)
                                                         gACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCtt                                                                               >  1:44037/1‑140 (MQ=255)
                                                          aCAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTc                                                                              >  1:729101/1‑140 (MQ=255)
                                                            aaaaaaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTg                                                                            <  2:242165/140‑1 (MQ=255)
                                                            aaaaaaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTg                                                                            <  1:760156/140‑1 (MQ=255)
                                                              aaaaaaGGCGACTCATCTGTCGCCTTAAAAACCAGTTTGTCAGCGCCGTCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGcc                                                                          <  2:325831/140‑1 (MQ=255)
                                                              aaaaaaGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAAATGGGTAACTCTTCATAGGTGTACGGCTCGCCTTCTGcc                                                                          >  2:319455/1‑140 (MQ=255)
                                                                      cGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                                                  <  2:729101/140‑1 (MQ=255)
                                                                      cGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                                                  <  2:1085571/140‑1 (MQ=255)
                                                                      cGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTg                                                                  <  2:571333/140‑1 (MQ=255)
                                                                        aCTCATCAGTCGCCTTAAAAATCAGGTTGCCAGCGCCCCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCa                                                                <  1:428465/140‑1 (MQ=255)
                                                                            atcaGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTc                                                            <  1:649376/140‑1 (MQ=255)
                                                                                 tCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAatga                                                       <  1:552429/140‑1 (MQ=255)
                                                                                    ccTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATgc                                                    >  1:855893/1‑140 (MQ=255)
                                                                                                 tttGCCAGCGCCGCCTTCTGCGACGCTACAAAGGATTCGCTTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGt                                       <  2:342490/140‑1 (MQ=255)
                                                                                                      cAGCGCCGCCTTCTGTGTCGCTCCACTGGCTTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtcatca                                  <  1:319455/140‑1 (MQ=255)
                                                                                                      cAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGtcatca                                  <  2:855893/140‑1 (MQ=255)
                                                                                                        gcgcCGCCTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACt                                <  2:19949/140‑1 (MQ=255)
                                                                                                          gccgccTTCTGCGTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCAGCACTTCTATGATGCGCCCGTATTCGGTCATCACTAc                              >  1:477278/1‑140 (MQ=255)
                                                                                                                      gTCGCTACAATGGATTCGATTCC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGt                  <  2:43483/140‑1 (MQ=255)
                                                                                                                                tGGATTCGATTCC‑C‑CCTCGGGCTAGAGCCAAGAAGTTGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCa        <  2:477278/140‑1 (MQ=255)
                                                                                                                                    ttcgattcC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCCGTCATCACTACATTGATGTCGATCTCTGCGGCAGAGt    >  1:516667/1‑140 (MQ=255)
                                                                                                                                     tcgattcC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTc   >  1:56018/1‑140 (MQ=255)
                                                                                                                                      cgattcC‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCt  <  2:44037/140‑1 (MQ=255)
                                                                                                                                           |                                                                                                                                        
CAATAAACTGGCGCTGATATGGTTTCATGCCTTCGCTCCTCATCTTACTTTTCTACAGACAAAAAAAAGGCGACTCATCAGTCGCCTTAAAAATCAGTTTGCCAGCGCCGCCTTCTGCGTCGCTACAATGGATTCGATT‑C‑C‑CCTCGGGCCAGAGCCAACAAGATGAGTAGCTCTTCATGGGTGAACGGCTCGCCTTCTGCCGTCCCCTGCACTTCAATGATGCGCCCGTCTTCGGTCATCACTACGTTCATGTCGGTCTCTGCGGCAGAGTCT  >  NC_000913/3815741‑3816013

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A